backup my store?

I want to upgrade to zc1.5.4 and I am trying to do a backup by copying the public.html folder
I keep getting duplicate target file names when I do a download to my local computer
using Filezilla. I have tried another ftp client with the same result.
This all seems to have started when my hosting company stopped allowing clear text logins.
I know there's the admin folder, yes I have renamed it, but what other folders are under the public html folder that
need to be backed up.
I already have a copy of the SQL database saved.

If you only have a Zen Cart in your public_html then you need All the files and folders ( exceptions are cgi-bin, docs, extras, cache )
If you are getting a duplicate target file name then your ftp client is finding these files or folders on your PC and would have nothing to do with the login going from clear text to secure. the only things that change in that are, hostname, and you use PASSV ports rather than a single port to transfer date over,) the connection port doenst even change

Here is a screen shot of a Filezilla error.
I downloaded the includes folder and put it into a new empty folder called includes_backup, and got the error.
I checked and the file is on the server, I don't know where the target file came from.

What are all the names of the files in that template_default/sideboxes folder on your PC?

Do you have files in uppercase and lowercase filenames? If so, that might be the problem, since your PC might be seeing "tpl_specials.php" as the same name as "tpl_Specials.php" ... and if it's downloading tpl_Specials.php first and then tries to do tpl_specials.php it'll find that tpl_Specials.php is already there, and give you that error.

None of the Zen Cart template_default files have any uppercase letters in their filenames ... so if you've got uppercase letters in the filenames on your server, you'll want to deal with that.

Maybe the problem is something else, but frankly that's the only case I've ever encountered unexpected duplicates ... unless of course I did indeed have duplicates already for some reason.

Alternative: Is your hosting company modern enough to have a File Manager tool that will let you zip up your ZC files on the server ... so you could then download that zip and be done with it? Your host should be able to help you with that.

ken1:

Here is a screen shot of a Filezilla error.
I downloaded the includes folder and put it into a new empty folder called includes_backup, and got the error.
I checked and the file is on the server, I don't know where the target file came from.

The message 'The target file already exists' should only be triggered if -and only if- that file actually exists on your local I:\ drive.

So, it must have been downloaded previously - files don't appear out of the blue from nowhere unless some application creates them in the background - and that's unlikely.

I simply do my backups by creating a local folder in /var/www/mysite (I am using Linux) and sftp all and every file into that folder. This way I have an identical copy of all files which exist on the server. In addition I create a compressed copy of the DB (using phpMyAdmin) and also pop it into the folder /var/www/mysite for safe keeping. The lot is then zipped again and the resulting zip file is transferred onto another drive on a different computer - just to be sure to be sure.....

Discovered the issue,
Connection dropped after the cache was created, auto reconnected and then because it started writing the file and connection was dropped it then it started to rewrite the file it was on when connection dropped. so infact it was seeing a target file,

I guess that means the problem was a bad internet connection, or maybe a webserver logging them out during download.